Stool microbiota composition is associated with the prospective risk of Plasmodium falciparum infection

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Yooseph, Shibu ^a   Kirkness, Ewen F ^a   Tran, Tuan M ^b   Harkins, Derek M ^a   Jones, Marcus B ^a   Torralba, Manolito G ^a   O'Connell, Elise ^b   Nutman, Thomas B ^b   Doumbo, Safiatou ^c   Doumbo, Ogobara K ^c   Traore, Boubacar ^c   Crompton, Peter D ^b   Nelson, Karen E ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

^c Sociétés   (Mali)

Author keywords

16S rRNA gene sequencing; Gut microbiota; Human; Malaria; Plasmodium falciparum; Prospective cohort; Stool microbiota

Indexed keywords

RNA 16S; BACTERIAL RNA;

ADOLESCENT; ADULT; ARTICLE; BIFIDOBACTERIUM; CHILD; COHORT ANALYSIS; COMPARATIVE STUDY; CONTROLLED STUDY; DISEASE TRANSMISSION; ENDEMIC DISEASE; FEBRILE MALARIA; FECES ANALYSIS; FECES MICROFLORA; FEMALE; HUMAN; INCIDENTAL FINDING; INFANT; INFECTION RISK; INTESTINE FLORA; LONGITUDINAL STUDY; MAJOR CLINICAL STUDY; MALARIA; MALARIA FALCIPARUM; MALE; MALIAN; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; PERSISTENT INFECTION; PRESCHOOL CHILD; PROSPECTIVE STUDY; RNA SEQUENCE; RUMINOCOCCACEAE; SPECIES COMPOSITION; STREPTOCOCCUS; URINALYSIS; BACTERIUM; BLOOD; CLASSIFICATION; EPIDEMIOLOGY; FECES; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MALI; MICROBIOLOGY; MICROFLORA; PARASITOLOGY; PROCEDURES; RISK FACTOR; SEQUENCE ANALYSIS; TRANSMISSION; YOUNG ADULT;

BACTERIA (MICROORGANISMS); MALIA; PLASMODIUM FALCIPARUM;

ADOLESCENT; BACTERIA; CHILD; CHILD, PRESCHOOL; FECES; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INFANT; MALARIA, FALCIPARUM; MALE; MALI; MICROBIOTA; PROSPECTIVE STUDIES; RISK FACTORS; RNA, BACTERIAL; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, RNA; YOUNG ADULT;

EID: 84939641167     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1819-3     Document Type: Article

References (47)

1. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312(5778):1355-9.
2. Human Microbiome Project C. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486(7402):207-14.
3. Human Microbiome Project C. A framework for human microbiome research. Nature. 2012;486(7402):215-21.
4. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59-65.
5. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature. 2012;486(7402):222-7.
6. Pop M, Walker AW, Paulson J, Lindsay B, Antonio M, Hossain M, et al. Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition. Genome biology. 2014;15(6):R76.
7. Subramanian S, Huq S, Yatsunenko T, Haque R, Mahfuz M, Alam MA, et al. Persistent gut microbiota immaturity in malnourished Bangladeshi children. Nature. 2014;510(7505):417-21.
8. Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, et al. Dietary intervention impact on gut microbial gene richness. Nature. 2013;500(7464):585-8.
9. David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-63.
10. Kamada N, Chen GY, Inohara N, Nunez G. Control of pathogens and pathobionts by the gut microbiota. Nature immunology. 2013;14(7):685-90.
11. Uematsu S, Fujimoto K, Jang MH, Yang BG, Jung YJ, Nishiyama M, et al. Regulation of humoral and cellular gut immunity by lamina propria dendritic cells expressing Toll-like receptor 5. Nature immunology. 2008;9(7):769-76.
12. Hall JA, Bouladoux N, Sun CM, Wohlfert EA, Blank RB, Zhu Q, et al. Commensal DNA limits regulatory T cell conversion and is a natural adjuvant of intestinal immune responses. Immunity. 2008;29(4):637-49.
13. Shulzhenko N, Morgun A, Hsiao W, Battle M, Yao M, Gavrilova O, et al. Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut. Nature medicine. 2011;17(12):1585-93.
14. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122(1):107-18.
15. Clarke TB, Davis KM, Lysenko ES, Zhou AY, Yu Y, Weiser JN. Recognition of peptidoglycan from the microbiota by Nod1 enhances systemic innate immunity. Nature medicine. 2010;16(2):228-31.
16. Ivanov II WHJ, Darce J, Hattori K, Shima T, Umesaki Y, Littman DR, et al. Gut-residing segmented filamentous bacteria drive autoimmune arthritis via T helper 17 cells. Immunity. 2010;32(6):815-27.
17. WHO World Malaria Report 2014 [ http://www.who.int/malaria/publications/world_malaria_report_2014/en/ ]
18. Marsh K, Kinyanjui S. Immune effector mechanisms in malaria. Parasite immunology. 2006;28(1-2):51-60.
19. Langhorne J, Ndungu FM, Sponaas AM, Marsh K. Immunity to malaria: more questions than answers. Nature immunology. 2008;9(7):725-32.
20. Tran TM, Li S, Doumbo S, Doumtabe D, Huang CY, Dia S, et al. An intensive longitudinal cohort study of Malian children and adults reveals no evidence of acquired immunity to Plasmodium falciparum infection. Clin Infect Dis. 2013;57(1):40-7.
21. Crompton PD, Moebius J, Portugal S, Waisberg M, Hart G, Garver LS, et al. Malaria immunity in man and mosquito: insights into unsolved mysteries of a deadly infectious disease. Annu Rev Immunol. 2014;32:157-87.
22. Goncalves BP, Huang CY, Morrison R, Holte S, Kabyemela E, Prevots DR, et al. Parasite burden and severity of malaria in Tanzanian children. New Engl J Med. 2014;370(19):1799-808.
23. Kwiatkowski DP. How malaria has affected the human genome and what human genetics can teach us about malaria. Am J Hum Gene. 2005;77(2):171-92.
24. Turner L, Lavstsen T, Berger SS, Wang CW, Petersen JE, Avril M, et al. Severe malaria is associated with parasite binding to endothelial protein C receptor. Nature. 2013;498(7455):502-5.
25. Yilmaz B, Portugal S, Tran TM, Gozzelino R, Ramos S, Gomes J, et al. Gut Microbiota Elicits a Protective Immune Response against Malaria Transmission. Cell. 2014;159(6):1277-89.
26. Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, et al. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A. 2008;105(6):2117-22.
27. Riley EM, Wagner GE, Akanmori BD, Koram KA. Do maternally acquired antibodies protect infants from malaria infection? Parasite Immunol. 2001;23(2):51-9.
28. Holmes I, Harris K, Quince C. Dirichlet multinomial mixtures: generative models for microbial metagenomics. PloS one. 2012;7(2):e30126.
29. Weiss GE, Traore B, Kayentao K, Ongoiba A, Doumbo S, Doumtabe D, et al. The Plasmodium falciparum-specific human memory B cell compartment expands gradually with repeated malaria infections. PLoS pathogens. 2010;6(5):e1000912.
30. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol. 2007;5(7):e177.
31. Jumpstart Consortium Human Microbiome Project Data Generation Working G. Evaluation of 16S rDNA-based community profiling for human microbiome research. PloS one. 2012;7(6):e39315.
32. Chassard C, de Wouters T, Lacroix C. Probiotics tailored to the infant: a window of opportunity. Curr Opin Biotechnol. 2014;26:141-7.
33. Gritz EC, Bhandari V. The human neonatal gut microbiome: a brief review. Frontiers in pediatrics. 2015;3:17.
34. Jain N, Walker WA. Diet and host-microbial crosstalk in postnatal intestinal immune homeostasis. Nat Rev Gastroenterol Hepatol. 2015;12(1):14-25.
35. Oozeer R, van Limpt K, Ludwig T, Ben Amor K, Martin R, Wind RD, et al. Intestinal microbiology in early life: specific prebiotics can have similar functionalities as human-milk oligosaccharides. Am J Clin Nutr. 2013;98(2):561S-71.
36. Sela DA, Mills DA. Nursing our microbiota: molecular linkages between bifidobacteria and milk oligosaccharides. Trends Microbiol. 2010;18(7):298-307.
37. Galili U, Mandrell RE, Hamadeh RM, Shohet SB, Griffiss JM. Interaction between human natural anti-alpha-galactosyl immunoglobulin G and bacteria of the human flora. Infect Immun. 1988;56(7):1730-7.
38. Doumbo S, Tran TM, Sangala J, Li S, Doumtabe D, Kone Y, et al. Co-infection of long-term carriers of Plasmodium falciparum with Schistosoma haematobium enhances protection from febrile malaria: a prospective cohort study in Mali. PLoS neglected tropical diseases. 2014;8(9):e3154.
39. Baird JK, Bangs MJ, Maguire JD, Barcus MJ. Epidemiological measures of risk of malaria. Meth Mol Med. 2002;72:13-22.
40. Dembele M, Bamani S, Dembele R, Traore MO, Goita S, Traore MN, et al. Implementing preventive chemotherapy through an integrated National Neglected Tropical Disease Control Program in Mali. PLoS neglected tropical diseases. 2012;6(3):e1574.
41. Landoure A, Dembele R, Goita S, Kane M, Tuinsma M, Sacko M, et al. Significantly reduced intensity of infection but persistent prevalence of schistosomiasis in a highly endemic region in Mali after repeated treatment. PLoS neglected tropical diseases. 2012;6(7):e1774.
42. Katz N, Chaves A, Pellegrino J. A simple device for quantitative stool thick-smear technique in Schistosomiasis mansoni. Revista do Instituto de Medicina Tropical de Sao Paulo. 1972;14(6):397-400.
43. Mejia R, Vicuna Y, Broncano N, Sandoval C, Vaca M, Chico M, et al. A novel, multi-parallel, real-time polymerase chain reaction approach for eight gastrointestinal parasites provides improved diagnostic capabilities to resource-limited at-risk populations. Am J Trop Med Hyg. 2013;88(6):1041-7.
44. Gevers D, Knight R, Petrosino JF, Huang K, McGuire AL, Birren BW, et al. The human microbiome project: a community resource for the healthy human microbiome. PLoS Biol. 2012;10(8):e1001377.
45. Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009;75(23):7537-41.
46. Gong L, Maiteki-Sebuguzi C, Rosenthal PJ, Hubbard AE, Drakeley CJ, Dorsey G, et al. Evidence for both innate and acquired mechanisms of protection from Plasmodium falciparum in children with sickle cell trait. Blood. 2012;119(16):3808-14.
47. Mangano VD, Kabore Y, Bougouma EC, Verra F, Sepulveda N, Bisseye C, et al. Novel insights into the protective role of haemoglobin S and C against Plasmodium falciparum parasitaemia. J Infect Dis. 2015;212(4):626-34.